Bug 585318 – dev-haskell/bio-0.5.3-r1 : setup: At least the following dependencies are missing:

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Toralf Förster 2016-06-07 16:28:47 UTC]

./setup configure --ghc --prefix=/usr --with-compiler=/usr/bin/ghc --with-hc-pkg=/usr/bin/ghc-pkg --prefix=/usr --libdir=/usr/lib64 --libsubdir=bio-0.5.3/ghc-7.10.3 --datadir=/usr/share/ --datasubdir=bio-0.5.3/ghc-7.10.3 --ghc-option=-j1 --ghc-option=-optc-march=native --ghc-option=-optc-O2 --ghc-option=-optc-pipe --ghc-option=-optl-Wl,-O1 --ghc-option=-optl-Wl,--as-needed --disable-executable-str
Configuring bio-0.5.3...
setup: At least the following dependencies are missing:
old-time -any
 * ghc-pkg check: 'checking for other broken packages:'
 * ERROR: dev-haskell/bio-0.5.3-r1::gentoo failed (configure phase):


$ cat emerge-info.txt
  -----------------------------------------------------------------

  This is an unstable amd64 chroot image (named amd64-plasma-unstable_20160606-203805) at a hardened host acting as a tinderbox.

  -----------------------------------------------------------------

  make.conf: USE="sse2 pax_kernel xtpax -cdinstall -oci8 -bindist avx cdb cdda cgi designer dot egl -evdev extraengine ffmpeg -fontconfig gles2 gnomecanvas gnutls -gtk2 help ipv6 ithreads kerberos logrotate mikmod mng mod -mp4 mpeg3 mta ncurses nss ogg openexr png qml sddm snmp source ssh ssh-askpass ssse3 -svg swscale -system-jpeg system-libs system-libvpx threads tls truetype uml v4l2 vaapi -vala webgl webstart wma -xetex -xmp xz"

  -----------------------------------------------------------------

Portage 2.3.0_rc1 (python 3.4.3-final-0, default/linux/amd64/13.0/desktop/plasma, gcc-5.3.0, glibc-2.23-r2, 4.5.6-hardened x86_64)
=================================================================
System uname: Linux-4.5.6-hardened-x86_64-Intel-R-_Core-TM-_i7-3770_CPU_@_3.40GHz-with-gentoo-2.2
KiB Mem:    16157888 total,   3222672 free
KiB Swap:   16777212 total,  16729304 free
Timestamp of repository gentoo: Tue, 07 Jun 2016 13:22:09 +0000
sh bash 4.3_p42-r2
ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1
app-shells/bash:          4.3_p42-r2::gentoo
dev-lang/perl:            5.24.0-r1::gentoo
dev-lang/python:          2.7.11-r2::gentoo, 3.4.3-r7::gentoo
dev-util/cmake:           3.5.2-r1::gentoo
dev-util/pkgconfig:       0.29.1::gentoo
sys-apps/baselayout:      2.2::gentoo
sys-apps/openrc:          0.21::gentoo
sys-apps/sandbox:         2.10-r2::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69-r2::gentoo
sys-devel/automake:       1.13.4-r1::gentoo, 1.14.1-r1::gentoo, 1.15-r2::gentoo
sys-devel/binutils:       2.25.1-r1::gentoo
sys-devel/gcc:            5.3.0::gentoo
sys-devel/gcc-config:     1.8-r1::gentoo
sys-devel/libtool:        2.4.6-r2::gentoo
sys-devel/make:           4.2-r2::gentoo
sys-kernel/linux-headers: 4.6::gentoo (virtual/os-headers)
sys-libs/glibc:           2.23-r2::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://rsync.gentoo.org/gentoo-portage
    priority: 1

local
    location: /usr/local/portage
    masters: gentoo
    priority: 2

ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c"
CXXFLAGS="-march=native -O2 -pipe"
DISTDIR="/var/tmp/distfiles"
EMERGE_DEFAULT_OPTS="--verbose-conflicts --color=n --nospinner --tree --quiet-build"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync network-sandbox parallel-fetch preserve-libs protect-owned sandbox sfperms strict test-fail-continue unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://ftp.uni-erlangen.de/pub/mirrors/gentoo rsync://mirror.netcologne.de/gentoo/ ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gor.bytemark.co.uk/gentoo/ rsync://ftp.snt.utwente.nl/gentoo"
LANG="en_US.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j1"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git"
PORTAGE_TMPDIR="/var/tmp"
USE="X a52 aac acl acpi alsa amd64 avx berkdb bluetooth branding bzip2 cairo cdb cdda cdr cgi cli consolekit cracklib crypt cups cxx dbus declarative designer dot dri dts dvd dvdr egl emboss encode exif extraengine fam ffmpeg firefox flac fortran gdbm gif glamor gles2 gnomecanvas gnutls gpm gtk help iconv ipv6 ithreads jpeg kde kerberos kipi lcms ldap libnotify logrotate mad mikmod mmx mmxext mng mod modules mp3 mpeg mpeg3 mta multilib ncurses nls nptl nss ogg openexr opengl openmp pam pango pax_kernel pcre pdf phonon plasma png policykit ppds qml qt3support qt4 qt5 readline sddm sdl seccomp semantic-desktop session snmp source spell sse sse2 ssh ssh-askpass ssl ssse3 startup-notification swscale system-libs system-libvpx tcpd threads tiff tls truetype udev udisks uml unicode upower usb v4l2 vaapi vorbis webgl webstart widgets wma wxwidgets x264 xattr xcb xcomposite xinerama xml xscreensaver xtpax xv xvid xz zlib" ABI_X86="64" ALSA_CARDS="hda-intel" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="evdev synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby20 ruby21" USERLAND="GNU" VIDEO_CARDS="intel i965" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account"
Unset:  CC, CPPFLAGS, CTARGET, CXX, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON

[Comment 1 Toralf Förster 2016-06-07 16:28:49 UTC]

Created attachment 436802 [details]
dev-haskell:bio-0.5.3-r1:20160607-161506.log

[Comment 2 Toralf Förster 2016-06-07 16:28:52 UTC]

Created attachment 436804 [details]
emerge-history.txt

[Comment 3 Toralf Förster 2016-06-07 16:28:55 UTC]

Created attachment 436806 [details]
environment

[Comment 4 Sergei Trofimovich (RETIRED) 2016-06-07 21:29:43 UTC]

Pushed as: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=0956ba9a9477be38e4f892bf4a8967f8e91875f4

Thank you!